Do we need to estimate effective transcriptome size before sequencing?

Question

[gayachit]

Hello everyone

We are thinking of doing whole transcriptome of some plants. I need to know do we need to have an estimate of the effective size of the transcriptome so that we know how much data coverage we need?? If yes, then how to do that? What are the pre-requisite things one should know before RNA-seq? Please help

Answer 1

[Carlo Yague]

Usually the coverage needed is estimated based on the genome size (easier to calculate than transcriptome size).

For instance, this table give crude coverage estimates based on genome size and application (differential expression analysis or transcript discovery).

[gayachit]

Thanks for the information carlo...